Not for Thom....

His hatred and resent of Tar Valon doesn't originate from this but from something far more despicable and cruel. Thom isn't a county bumpkin, and he's not irrational. He knows perfectly well the gentling had to happen.

He hates Aes Sedai because of the inhumane way the Red Ajah handled it (against the laws of the Tower, something Thom didn't know before Moiraine told him. Thom had rather concluded this was the way gentlings really were handled, and the Tower hid this). They never brought his nephew to Tar Valon, nor gave him the humane treatment Logain got after his gentling. Owyn was gentled illegally right there in his village, and left to the prejudices of his neighbours. Not only did he had to flee and died abjectly, but his young wife suffered so much of the experience she did too.

Thom made a scandal about it at Morgase's court and left, and the rest of the story is just implied, ie: Not only Morgase "knew" well the WT would never have done such a thing and had strict rules regarding gentling, but Elaida must have faked outrage and convinced Morgase Thom was a liar who sought to destroy the alliance between TV and Andor for his personal gain (ie: because he was jealous of Elaida's influence over the Queen, to whom he was the only advisor before her arrival).

It's extremely likely Elaida engineered the whole thing with her Red friends (her eyes-and-ears network in Andor probably heard rumours about Owyn and when she heard the name she jumped on the opportunity, or Galina wrote to Elaida about reports she got about a Merrilin man in a village suspected of being a channeller etc.) precisely to provoke this confrontation at court, that would obviously end with Thom being exiled, leaving her as Morgase's only advisor.

Moiraine has promised Thom she'd tell him what she knows about it, and given her quest it's likely Moiraine has investigated this because she was on the hunt for signs of the BA hunting down the Dragon. Moiraine can't possibly know this from the secret archives (the way Siuan knows, but only years after the Owyn gentling), which probably indicates that Moiraine discovered on her own what this gentling had really been about, enough to guess it wasn't the BA, which in turn strongly suggests Moiraine was able to trace it to Elaida, and puzzled out her motives.

I remain more or less convinced Moiraine and Siuan were the ones who secretely (and likely anonymously) denounced the "illegal gentlings" to the Amyrlin Marith Jaen, as soon as Sierin Vayu died. It think Moiraine's main motivation, aside from stopping the horrors the Red were committing, was to force the BA to stop using the radical Reds as a cover to kill men suspected of being the Dragon.

Another possibility is that Thom's scandal at court about the gentling of Owyn was overheard by Blue Ajah spies, and the Amyrlin was brought to investigate further because Elaida herself had reported nothing, or a version that didn't jive with the reports of the eye-and-ears about Thom's accusations, convicing Marith Jaen the Reds may truly be hiding something.